Most introgressions are present at low frequencies.

<p>Frequencies of introgressed regions defined as inclusive sets of overlapping individual introgressions. <b>A)</b> <i>san</i>-into-<i>yak</i>. <b>B)</b> <i>yak</i>-into-<i>san</i>. <b>C)</b> <i>tei</i>-into-<i>yak</i>. <b>D)</b> <i>yak</i>-into-<i>tei</i>.</p

Proportion of correctly identified simulated introgressions by Int-HMM.

<p>The HMM successfully identified over 80% of introgressions longer than 10kb for all directions of introgression. It consistently performed better at identifying homozygous introgressions (homo) than heterozygous (het) ones. Additionally, it identified higher percentages of introgressions between <i>D</i>. <i>yakuba</i> (<i>yak</i>) and <i>D</i>. <i>teissieri</i> (<i>tei</i>) than those between <i>D</i>. <i>yakuba</i> and <i>D</i>. <i>santomea</i> (<i>san</i>).</p

D-statistic variations (D [31,32] and f_d [71]) show evidence for admixture between <i>D</i>. <i>yakuba</i> (mainland, São Tomé hybrid zone—HZ—, and other islands—Bioko and Principe—) and <i>D</i>. <i>santomea</i> and between <i>D</i>. <i>yakuba</i> and <i>D</i>. <i>teissieri</i>.

<p>Note, that the negative numbers of D indicate that the average direction of the introgression goes from the population assigned as putatively recipient to the population assigned as putatively donor [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006971#pgen.1006971.ref071" target="_blank">71</a>].</p

Introgression tracts are generally small.

<p>Distributions of tract sizes. Note that tracts smaller than 500bp were not included in the analysis. <b>A)</b> <i>san</i>-into-<i>yak</i>. The distribution has been truncated to exclude a single large 959kb tract shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006971#pgen.1006971.s005" target="_blank">S5 Fig</a>. <b>B)</b> <i>san</i>-into-<i>yak</i>. <b>C)</b> <i>tei</i>-into-<i>yak</i>. <b>D)</b> <i>yak</i>-into-<i>tei</i>.</p

Fine scale mapping of genomic introgressions within the <i>Drosophila yakuba</i> clade

<div><p>The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, <i>D</i>. <i>santomea</i> and <i>D</i>. <i>yakuba</i> hybridize on the island of São Tomé, while <i>D</i>. <i>yakuba</i> and <i>D</i>. <i>teissieri</i> hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the <i>Drosophila yakuba</i> clade (<i>D</i>. <i>yakuba</i>, <i>D</i>. <i>santomea</i>), <i>D</i>. <i>teissieri</i>). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on <i>X</i> chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.</p></div

Percentage of genome introgressed between each species pair.

<p>Percentage of the genome that was introgressed for each line as determined by the cumulative length of introgression tracts identified by Int-HMM. <i>D</i>. <i>yakuba</i> has been divided into geographical populations where ‘ST: HZ’ refers to the São Tomé hybrid zone and ‘ST: Low’ to the lowlands of São Tomé. <b>A)</b> <i>yak</i>-into-<i>san</i> and <i>san</i>-into-<i>yak</i> introgressions. <b>B)</b> <i>yak</i>-into-<i>tei</i> and <i>tei</i>-into-<i>yak</i> introgressions.</p

<i>Treemix</i> results for the <i>D</i>. <i>yakuba</i> clade indicate gene flow has occurred among species of the <i>yakuba</i> clade.

<p><i>Treemix</i> trees with the best supported number of migration edges. <i>D</i>. <i>yakuba</i> has been split into four populations: “africa” (Cameroon, Kenya, Ivory Coast), “islands” (Príncipe and Bioko), “low_ST”(lowlands of São Tomé), and “hz_st”(hybrid zone on São Tomé). <b>A)</b> Autosomal tree with 4 migration edges. <b>B)</b> <i>X</i> chromosome tree with 2 migration edges. Other demographic scenarios are shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006971#pgen.1006971.s002" target="_blank">S2</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006971#pgen.1006971.s003" target="_blank">S3</a> Figs.</p

Raw data and analytical code Turissini et al. 2015

Raw data and analytical code Turissini et al. 201

Histoplasma H88: Reference genome

Histoplasma H88: Reference genom

Supplementary Tables: S1-S6 (Sepulveda et al. mBio 2017)

Supplementary Tables: S1-S6 (Sepulveda et al. mBio 2017